Bismark

Bismark Processing Report

/gscratch/scrubbed/sr320/0924/EPI-167_S10_L002_R1_001_val_1.20bp-trim.fq.gz and /gscratch/scrubbed/sr320/0924/EPI-167_S10_L002_R2_001_val_2.20bp-trim.fq.gz

Data processed at 07:08 on 2019-09-26


Alignment Stats

Sequence pairs analysed in total 24477306
Paired-end alignments with a unique best hit 10316162
Pairs without alignments under any condition 11770881
Pairs that did not map uniquely 2390263
Genomic sequence context not extractable (edges of chromosomes) 0

Cytosine Methylation

Total C's analysed 257754397
Methylated C's in CpG context 8600854
Methylated C's in CHG context 1106051
Methylated C's in CHH context 4727455
Methylated C's in Unknown context 34010
Unmethylated C's in CpG context 24449142
Unmethylated C's in CHG context 52390495
Unmethylated C's in CHH context 166480400
Unmethylated C's in Unknown context 540892
Percentage methylation (CpG context) 26.0%
Percentage methylation (CHG context) 2.1%
Percentage methylation (CHH context) 2.8%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 5105614 original top strand
CTOT 0 complementary to original top strand
CTOB 0 complementary to original bottom strand
OB 5210548 original bottom strand

Deduplication

Alignments analysed 10316162
Unique alignments 7536993
Duplicates removed 2779169
Duplicated alignments were found at 1780201 different positions

Cytosine Methylation after Extraction

Total C's analysed 131400242
Methylated C's in CpG context 4459870
Methylated C's in CHG context 517777
Methylated C's in CHH context 2510683
Unmethylated C's in CpG context 11908013
Unmethylated C's in CHG context 25936927
Unmethylated C's in CHH context 86066972
Percentage methylation (CpG context) 27.2%
Percentage methylation (CHG context) 2.0%
Percentage methylation (CHH context) 2.8%

M-Bias Plot